I have performed trinity assembly , now I want assess the quality of the the assembled transcript .. with the most closely related species of my plant
I have created database of annotated reference transcriptome
tuttu@kau:~/ngs/trinityrnaseq-2.1.1$ makeblastdb -in test.fasta -dbtype nucl Building a new DB, current time: 12/09/2015 17:59:24 New DB name: test.fasta New DB title: test.fasta Sequence type: Nucleotide Keep Linkouts: T Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 61538 sequences in 4.21683 seconds.
After that I tried to run megablast to align the known transcripts to the Trinity assembly:
This is the command used :
blastn -query ~/ngs/trinityrnaseq-2.1.1/trinity_output_data2/Trinity.fasta -db /home/jinu/ngs/trinityrnaseq-2.1.1/test.fasta -out Trinity_vs_test.blastn -evalue 1e-20 -dust no -task megablast -num_threads 2 -max_target_seqs 1 -outfmt 6
But my attempt was unsuccessful
it results in this error
command line argument error: Argument "out". File is not accessible: `test.blastn'